The Captain
by homesweethomicide13
Summary: It's been ten years since Jack was on Earth. When he returns, he finds that Torchwood has been rebuilt, and there is a new Captain sitting behind his desk.


**Title:** The Captain  
**Author:** homesweethomicide13  
**Rating:** T  
**Pairing:** No major pairing featured  
**Warning:** Bad language, maybe some violence and bloodshed  
**Disclaimer:** Torchwood does not belong to me. The members of Torchwood 4, however, do.  
**Summary:** It's been ten years since Jack was on Earth. When he returns, he finds that Torchwood has been rebuilt, and there is a new Captain sitting behind his desk.

**Spoiler Warning:** If you haven't seen Children of Earth at all, then I suggest you watch it before reading this. It IS set ten years after the end of Day Five, so there's no way to avoid any spoilers, unfortunately.

**The Captain**

Cool blue eyes focused on the screen showing the area outside, and fingers tapped away at a keyboard. The screen zoomed in on a particular man who was just standing there, staring around him in surprise. Sitting back in a chair that creaked in protest, a hand came up to the communications device in one ear, and a smile formed on a youthful face.

"Code zero-six-five." The voice held tones of amusement. "He's back."

*

Everything was back in place, perfectly rebuilt as though nothing had ever happened. He stared around him, unbelieving, trying to make sense of what he was seeing. Even that water tower had been rebuilt. Frowning slightly, he turned and jogged down to the spot where the tourist office had once been and, sure enough, even _that_ had been rebuilt. He ran his tongue over his dry lips and approached the door slowly. What was he honestly expecting if he went in there? It probably _was_ just a tourist office now, or something similar. The sign on the door read 'closed', but he tried the handle anyway surprised to find that it opened easily.

He couldn't believe his eyes when he stepped into the room beyond. Everything had been rebuilt to make an exact copy of the one that had been blown to bits. Even the outdated leaflets and newspaper clippings were included. He walked around to the other side of the desk and peered into the back room cautiously, but he found it empty. Turning around, he spotted the door release and pushed it with one finger, watching the tourist office door click closed, and with a hiss the secret passageway opened.

He was careful as he walked through the maze of tunnels down to the cog wheel door and stood in front of it before pressing the button on the wall that would open it. As he rolled back, the alarm sounded and the metal gates opened out for him, showing him what was beyond. His jaw dropped. Everything was exactly as he remembered – with a few improvements here and there. He strolled through into the main area and a grin formed on his face. This was fantastic! He briefly wondered if Gwen had something to do with this, or maybe Martha…

"About time." He froze at the unfamiliar voice, and spun around to face the owner. In fact, what he saw when he turned around were three complete strangers, two of them hanging back slightly. The one in front was obviously the ringleader, and this is the one that jumped down the handful of steps up to the main workstation deck, walking over to him and stopping just in front of him. It was a young man with chin-length sun-blonde hair and piercing blue eyes, wearing a long white coat. "What took you? We don't have all day, you know. Come on, follow me. There is someone who has been expecting you for quite some time." Without waiting for any word from him, the young man turned and jogged back up the stairs, sweeping past the other two. The younger one, another male, glanced at the blonde's retreating back and then at his companion, a woman with long dark hair tied back into a rough ponytail.

"Best not to keep the boss waiting." She said directly to him, and the younger man nodded his agreement. Sighing, he walked up the steps and followed the direction the blonde had taken. He frowned when he spotted the blonde in the doorway of his office – his _old_ office – and sped up his pace a little. He was curious as to who these people were, and he wanted to know what had happened to Gwen. Had she given up on Torchwood, too? He stopped in front of the blonde, and was about to start demanding answers when he held up a hand.

"I'm not the one who has been expecting you. Go on in." He gestured at the office beyond. Snapping his jaw shut, he pushed past him and walked into the office, stopping short in front of the desk when he saw the person sat behind it.

"Captain Jack Harkness." He swore that there was a hint of mockery in the voice when his name was spoken. "I've been waiting for this day for quite a long time." He ran his eyes over the person sat in _his_ chair, behind _his_ desk, in _his_ office. His first surprise had been the fact that it was, indeed, a young woman – with chin-length, ruffled brown hair with a sweeping fringe to the left, like his own. Her eyes were ice blue, similar to his own, but slightly colder. She was dressed in a black dress shirt with the sleeves fastened tight around her wrists, and faded blue jeans. Her feet were propped up on the desk, and so he could see that she wore dark brown boots, much like the ones he liked to wear, only hers were not tied properly.

"Who the hell are you, and who are these people? Where's Gwen?" He demanded sharply. Those ice cold eyes narrowed and she swung her feet off the desk, standing up and circling the desk so that they were standing face-to-face. He ignored the fact that she was nearly as tall as he was.

"We're Torchwood." She barked, sticking her hands into the pockets of her jeans. He noticed for the first time that she was wearing braces, although they remained hanging at her sides instead of up over her shoulders. "And you, Captain, are trespassing." He didn't stop his jaw from dropping. _He_ was trespassing? Surely they knew who he was? "Of course, I've been waiting for you to return, so I'll let it pass. Now, to answer your other question – Gwen is currently at home, with her husband and daughter, most likely watching TV on the sofa and listening to Rhys ramble on about trucking." A smirk crossed her face, and it was oddly familiar to him. "Perhaps you should meet the team." She side-stepped around him and walked out of the office, and sighing, he followed her.

The younger man and the woman were at workstations, tapping away at keyboards and completely focused on the screens in front of them. The blonde jogged up the stairs leading down to the medical bay, removing a pair of latex gloves and dumping them into a bin on his way.

"Captain, meet Dr Leo Murphy, Torchwood's medical examiner." She told him. Leo held out a hand, and Jack shook it cautiously. "That's Sarah Dawson, our leading alien tech expert." Sarah turned from her monitors and held up a hand in greeting. "And this youngster here is Dafydd Williams, son of Gwen and Rhys." Dafydd smiled and met Jack's eyes.

"Adopted son, but a Williams nonetheless." He explained. Jack was struggling to take all of this in. Not only was there a new Hub, a new Torchwood team, but now he'd learnt that Gwen had a son _and_ a daughter with Rhys. He turned back to this strange female who seemed to be in charge.

"What about you? You never told me your name." He asked with a raised eyebrow. She smirked again, and shrugged casually.

"You never told anyone yours." Something about the way her head inclined backwards as she met his eyes with a cold, knowing stare told Jack that she knew exactly who he was, down to his deepest, darkest secrets. He realized with a chill that she was giving him the exact same stare that he used on others. Suddenly she pulled her hands from her pockets and slammed them together. "Drinks! I'm sure you're curious about, well… everything, so I'll answer your questions." The smirk vanished from her face. "But not here. Leo! Get my coat." He nodded and darted into her office to retrieve said article of clothing. "Ready for another surprise, Captain?" Before he could question her, Leo reappeared holding a dark coat, which he slipped onto her shoulders. Jack's eyes widened as he took in the dark blue-black colour, the familiar stitched symbols on the arms, and the stripes on the shoulders.

"That's…"

"A slightly different version of your own military coat, yes." She finished for him. "I rather like it, don't you? Now, let's get going." She turned to the team. "Sarah, I want the final analysis of that tech on my desk tomorrow morning. Dafydd, see if you can retrieve those files that were 'lost', we might need them. Leo… you know what to do." He nodded and saluted before darting back into her office. "Leo deals with all my paperwork, files it in the archives and makes sure everything is in order. I'd be swamped in it if it wasn't for him." She led the way out of the Hub, grabbing a set of keys from the wall in the tourist office on the way out.

When he followed her to the car park, she held out the keys and pressed a button, unlocking the car from a distance. Jack stopped dead when he noticed which car had flashed its lights, indicating it was now open.

"You have the same SUV." He stated bluntly, causing her to turn around and fix him with an amused smile. "I thought it was lost."

"It was. This isn't the same." She clicked a button and red lights flashed along the edges of the front and back windscreen. "Yours had blue, if I remember correctly." He couldn't help but laugh a little at the tiny difference, and she grinned. "Now get in, we have a lot to discuss."

*

Jack had once said that Owen's driving was bad. He now took it back – this woman drove like a complete maniac. Still, he supposed it wasn't exactly going to do him any serious harm. They pulled up outside a bar and she turned off the engine, climbing out of the SUV in an oddly graceful manner. He followed her, watching as she kicked open the door and declared in a loud voice that she was Torchwood and it was time for everybody to leave. He shuddered when he realized just how much like Captain John she was.

Once everyone had cleared out, she jumped over the bar and grabbed the nearest bottle of whiskey, pouring out a glass for herself. Without a word she filled a glass with water and slammed it down onto the bar in front of Jack. He raised his eyebrows but said nothing as she jumped back over the bar and sat down, gesturing for him to join her. She downed the first glass in one and refilled it, but left it untouched. She turned to him, her expression serious, and he braced himself for what was to come.

"So, where do you want me to start?" He took a swig of his water and sighed.

"What happened to the Hub? You know, after I left." She smirked.

"That's an easy one. Gwen was furious that you'd left, once she got over her initial grief of losing you. Martha Jones visited, she came the moment she could, and after about a week, Gwen and Martha made the decision to rebuild the Hub in honour of the losses Torchwood 3 had suffered in recent months." Jack felt something pull at his heart. Those losses included Ianto. "Martha called in some help, people she'd met in a time of crisis and who helped to save the world from the Daleks." Jack's eyebrows shot up, and she grinned. "Do the names Mickey Smith and Sarah Jane Smith mean anything to you, Jack?"

"The children of time. They really gathered to help rebuild the Hub?" She nodded.

"Yep. It took time, and Martha pulled some strings at UNIT to get us some extra pairs of hands, but it wasn't even halfway done when we got a surprise visit from a very special man. You know him quite well, actually. You've even travelled with him." Jack had been about to take another sip of water, but the hand holding the glass froze before it got to his mouth. "I was quite pleasantly surprised to see your Doctor, Jack. I figured after the 456 incident that he was tired of saving this little planet. Apparently not. He stuck around for a little while, helping out here and there. He rebuilt the rift manipulator, you know. Probably couldn't have done it without him."

"I looked for him, out in the galaxies. I searched everywhere." Jack murmured in disbelief.

"And all that time he was right here on Earth." She cut in. "Maybe you shouldn't have left, after all." Ignoring the look on Jack's face, she continued. "Once the Hub was rebuilt it was obvious that we were going to need a new team to keep it running. Gwen, Martha and Mickey offered to stick around until I'd found myself some new recruitments, which was probably for the best considering I didn't find my first one until five years later."

"Wait, wait. Back up a second. Why were you in charge?" He demanded. "Besides, you look young, so you must have been even younger back then."

"It's true that only ten years have passed since you were last here, Jack, but my age has nothing to do with it. I was automatically put in charge the moment your feet left Earth's soil." Her cold eyes fixed on him in a stare he tried not to wither under. "You see, Jack, there are things that were kept secret from you, right from the very beginning. The moment Torchwood recruited you, they were trying to figure out how you couldn't die. They wanted the secret behind your immortality."

"They weren't going to get it. It was by chance that it happened – one wish made by a girl with too much power to control and I can never die." He snapped.

"Oh I know all about that." She said coolly. "I know about Rose, and the Time Vortex, and Satellite 5. I know much more than you'd care to believe, Jack." She took a swig of her drink. "When technology was beginning to advance a little more, Torchwood ran a series of medical tests on you. Do you remember?" He nodded. How could he forget? Some of them were pure torture. "Well, what they were trying to do was clone your ability to live forever. They took various cells from your body, took your DNA and tried to copy it. Of course, all attempts failed and for a while they gave up." The smile that crossed her face was almost dark, and Jack didn't particularly like it. "But then they had a revelation. A member of Torchwood 1 came to the labs with the theory of mixing your DNA with another human's, and perhaps if they cancelled enough of the chromosomes from the other DNA, then yours would take over and they'd have a successful copy of your immortality."

"What?" He hissed. "Did it work?"

"The member who thought up the idea volunteered her DNA to be used as a test, and the procedures that followed were long and trying. They fused the DNA together, cancelled out most of the chromosomes from her DNA with some alien tech they'd picked up somewhere, and hoped for the best." She swirled the whiskey in the glass, staring down at the dark liquid. "Not long after that, the Cybermen invaded and we all know how that chapter ended. Torchwood 1 was shut down, destroyed, and the labs were turned into the cyber conversion units. The woman who'd given her DNA was lost in the battle, as were most of the scientists and researchers, but a few of them survived. Well, when I say survived…"

"Look, I'm all for history lessons but I think it's time you got to the point of this." Jack cut in, getting impatient. She fixed her cold eyes on him again and grinned.

"Oh, but I am." She told him. "You remember Ianto Jones, don't you?" Jack averted his eyes as a jolt of pain shot through his chest. Of _course_ he remembered. He'd never forget. He made a promise, and he was going to keep it. "He had a partially converted girlfriend, Lisa. He brought her down here, to Cardiff, hoping to use Torchwood 3 to help her. She ended up being killed by you and the others, but it was worth a shot, I suppose. I was also at Torchwood 1 when the invasion happened. Ianto helped me escape, and in return I helped him find a way to get into Torchwood 3 so that Lisa could be kept in a safe place."

"What?!"

"Who do you think coaxed that pterodactyl into that warehouse while he was out convincing you to hire him? I told him where the dinosaur was, told him where you were that night, and I'm sure you know all too well what happened after that." She grinned at the expression on his face. "Oh don't give me that look. Ianto was positive that Lisa was still human, and since he'd also pulled _me_ from the wreckage of Torchwood 1, I felt that I owed it to him to help. If I'd known that Lisa was going to try and build a Cyberman army in the Hub, I probably wouldn't have made the effort."

"Ianto never mentioned you."

"He wasn't ever allowed to." There were no smiles or laughter now. He could tell from her eyes that this was a time to be deadly serious. "He had to swear secrecy, from even before he'd met me. After helping with Lisa, I was relocated to the south of England, where I lived with two guardians. Ianto contacted them once a month, detailing the events of Torchwood 3. He and my guardians set up a system that would only be put into action as a result of Ianto's death. If we didn't receive any form of communication from him after six months, I was to move to Cardiff and enter Torchwood 3."

"Six months… that's when I left…" Jack murmured. "But why? What is so important about you? And why couldn't Ianto speak of you?"

"All of the Torchwood 1 members involved were sworn to secrecy, even if they never even got the chance to see me. Most of them just knew me as a number, a code. Ianto was just a junior researcher, as you may remember, so he was never allowed into the labs, but he knew of me." Jack had set down his glass of water. He knew his hands were trembling, and something told him he knew where this conversation was going. "Very few members thought of me as a person until the moment I opened my eyes to the world." She leant in closer, a creepy smile forming on her face.

"Who are you?" Jack whispered, feeling a slight hint of fear building up.

"I'm _you_." She replied in a quiet murmur. After letting that sink in for a while, she leant back and grinned. "Well, sort of. It's mostly your DNA, and I most certainly take after you in appearance, but there is other DNA floating around somewhere. I'm the only successful case from Torchwood 1. I'm not sure _how_ successful considering by the time I was old enough for them to start running tests, all hell broke loose and the scientists got themselves killed." Jack couldn't believe it. All those things that had seemed so familiar to him – the smirk, the smug, confident attitude, the hair, the eyes, the dress code… it was all _him_. With a shock he realized that this is how everyone must see him from the outside. He remembered the fear that had been building up and wondered if everyone he'd met had felt that same fear on meeting him. "The Doctor saw it straight away, but he's smart enough not to talk about it unless we're in private. Ianto knew who I was from the moment he freed me from the lab. He swore to never mention me to you, for both our protection."

"For our protection?"

"If you had known I existed, what would you have done, Jack? Would you have searched for me? What if someone intercepted and found me first? What would you do then?" He had no answer for her. "I had an alias, whilst I was living in England. A totally new name, and my guardians had to pose as my adoptive parents – they would have posed as my _actual_ parents, but this isn't the 51st century. Men can't get pregnant yet." Jack smiled at that.

"So you know of the 51st century?"

"I told you. I know everything." She replied with a grin. "Besides, have to learn a bit about my heritage, right? I tell you, these 51st century pheromones can do wonders when you want them to." Frowning, Jack leant forward and breathed deep, grinning when he recognized the scent as very similar to his own.

"So you've inherited some 51st century traits. Anything else?" She knew what he was asking. He wanted to know if she could age, if she could die.

"I don't know." She shrugged. "I dropped the alias when I moved here. No point hiding away under that name."

"So what is your real name?"

"I don't tell people that, Jack. I have several names, but I stick to one more often than others, because I enjoy it. Plus, it tells people who I am without actually telling them. Keeps them wondering." She turned and leant back against the bar. "I like a bit of mystery, don't you?"

"Alright, so what do I call you?"

"Listen, I have to get back to the Hub and kick Dafydd out before Gwen phones me up asking where her son is at this time of night." She finished her drink and replaced the bottle on the other side of the bar, sticking a couple of notes underneath it. She noticed his confused expression and explained. "Monty – he owns this place – is used to me running in and kicking everyone out. I like to give him something for the trouble." Hopping back over the counter, she reached into a pocket of her coat and put a piece of paper down on the bar in front of him. It appeared to be plain. "That should tell you all you need to know, Captain." Without waiting for him to pick it up, she darted out of the bar.

Staring after her in confusion, and not forgetting that she still hadn't told him her name, he turned his attention to the blank paper. He picked it up and held it to the light, trying to see if pale or invisible ink had been used. As he stared at it, however, words began to form, written in black ink. The Torchwood logo was in the top left corner, followed by the word 'Cardiff' in the bottom right corner. A number for a mobile phone was scrawled along the bottom, and he assumed it would belong to her. But it was the words that formed in the middle that consumed all of his attention. Those three simple words were the most important things in Jack's world at that particular moment.

Captain Felix Harkness.

It was her name.

* * *

_Some secrets should be told._

Felix stood on a roof on the edge of the city, high up off the ground. It was most certainly a long way down and falling would end in fatal injuries, and most likely sudden death. She liked standing on roofs, especially on windy days. Just getting that thrill of being so far up, so much closer to the sky than anyone down below, was worth the risk of falling. She'd read somewhere that Jack liked standing on roofs, too. Perhaps it was something she'd inherited from him.

_Some secrets should be heard._

Jack lay on one of the Hub sofas, wide awake as usual. It had passed midnight a long time ago, and there was no rift activity whatsoever. It was too quiet. He was used to alarms sounding every hour, tired people rushing through the Hub to collect the right gear for the job. He was used to Ianto curled up at his side, sleeping peacefully, unaware that his partner was still awake, and always would be. He didn't need to sleep as much as the average person. And when he did sleep, nightmares plagued him. He turned his head to stare at the workstation that had once belonged to Tosh. The screens were on, monitoring the rift. He silently pleaded for the rift to drop something harmless into the city just to give him something to do.

_And some secrets…_

With a smile, Felix spread out her arms either side of her, feeling the wind rush by, lifting the tails of her coat and sweeping the hair away from her face and neck. She closed her eyes and tilted herself forward, leaning precariously over the edge of the roof. The smile became a grin, and she jolted forward, falling down to the ground below. She landed with a sickening crunch, a faint smile still visible on her face as blood pooled around her.

… _should remain secrets._

With an exaggerated gasp, life danced back into her eyes and her whole body jerked back into action.

Taking a few deep breaths, she laughed as she picked herself up off the ground, feeling bones snapping back into place as she did so. She pulled a cloth from an inside pocket and wiped the blood from her face before checking if the wound had healed itself yet. It had.

"Shit. That gets better every time." She murmured to herself. "Alright, back to work."

* * *

_**Author's Note:** Okay, this was originally just going to be a one-shot or maybe a two-shot (I had the best idea for a scene with Felix, Jack and coffee but I couldn't fit it in here), but if you people want to read more into this new Torchwood, then let me know and I may very well make it into a full story. Just a couple of things to clear up first:_

_- Felix is SUPPOSED to be exactly like Jack, so I'm not just copying his character for the sake of it. She's not a "Mary-Sue", so please don't bother saying that._

_- I know the beginning of this is kinda like Everything Changes, with Jack walking in and being introduced to a team and then the boss taking him out for a drink, BUT that wasn't intentional and I only realized how similar it is when I'd finished, and I didn't want to go back and change it. _

_- Dafydd was originally going to be the baby that Gwen was expecting at the end of Children of Earth Day 5, but due to timespans etc he would only be ten years old by now and that just isn't realistic, so I ended up making him their adopted son. If I continue on with this story I might dig deeper into that and explain it further, but until then, you'll just have to accept it. XD_

_I can't think of anything else to add to the list, so... please review and let me know what you think. If I do decide to make it a full length story, updates might not be too regular as I already have two Doctor Who and Torchwood crossover stories on the go and need to focus on those. Hope you enjoyed the story! I went for an original idea, hope it worked. I haven't seen any stories like this yet, anyway. _

_- homesweethomicide13_


End file.
